Daniel McGowan was in the yard of the Federal Correctional Institution in Sandstone, Minn., when his name rang out over the loudspeaker. It had been eight months since he first reported to the low-security prison to start a seven-year sentence for conspiracy and arson. To pass the time, he worked as an orderly in the prison psychology department, took correspondence classes and exercised.

Sandstone, located nearly smack-dab in the middle of the country, was about as far removed as McGowan could be from his wife, Jenny Synan, in New York and from his former compatriots in the Earth Liberation Front in Oregon, with whom he had been caught in a national law enforcement sweep. But he still kept in touch with the outside world, writing passionate articles about the environment and prisons for publications like the Earth First! Journal. He was allotted 300 minutes of phone time a month. And on the rare occasions when Synan could get away from work, she would come see him. In the prison’s visiting room, they would hug and kiss and play board games together.

He was looking forward to such a visit when the loudspeaker told him to report to the prison’s shipping and receiving department. It was the day before his second wedding anniversary in May 2008, and he assumed that he was being called in for some routine matter. Perhaps the package full of books he had recently mailed to his wife had been returned for insufficient postage, he thought.

Instead, a prison staffer handed McGowan two boxes and told him to fill them up with his possessions. He was the one being shipped. When he asked his case manager where he was being taken, he was thrown in a cell.

He headed south the next day, still unsure of his destination. “When I got on the bus, they told me ‘Marion,'” McGowan says.

After the supermax in Florence, Colo., opened in 1994, Marion remained in use as a maximum-security prison. In 2006, it was renovated, expanded and downgraded to a medium-security facility. But in March 2008, it quietly regained some of its supermax identity — and its status as an experimental prototype for the prison system — when the Federal Bureau of Prisons established within its walls a secretive wing known as a Communication Management Unit, where prisoners are held under tight restrictions. Inmates call it “Little Guantanamo.” This is where McGowan was headed.

Forty-two prisoners are currently in the CMU at Marion. Another 43 are in a similar facility in Terre Haute, Ind., that was built two years earlier. The special units were developed as part of the federal government’s crackdown on terrorism following 9/11. Particularly after Lynne Stewart, the former defense attorney for the Blind Sheik, Omar Abdel-Rahman, was convicted in 2005 of covertly sending messages to her client’s followers in Egypt, the Bureau of Prisons was determined to create a new form of incarceration to monitor inmates’ every contact with the outside world. When the CMUs were first opened, nearly all of their inmates were Muslim men.

Unlike at Guantanamo, the prisoners in these CMUs are not being held indefinitely. But they are subjected to unusual restrictions: only two 15-minute phone calls a week, heavily monitored mail and eight hours of visitation a month. Inmates are restricted in how many times a week they can hold group prayers. Their movements and conversations are recorded at all times. Critics have described the conditions as psychologically debilitating.

Some of the inmates currently being held in CMUs are people like John Walker Lindh, who fought with the Taliban against U.S. forces in Afghanistan. Many others have only tenuous connections to terrorism, however. Some of their crimes are merely hypothetical. Yassin Aref, an Albany, N.Y., imam, for example, was convicted of witnessing a fake loan for a Stinger missile to be used against the Pakistani ambassador in New York. According to Paul Wright, the ex-con founder of Prison Legal News, most of the prisoners being housed in CMUs “aren’t even the second- and third-tier prisoners in the war on terror. These are like the sixth and seventh tier.”

Others have no publicly known connection to terrorism at all, beyond sharing a religion with the perpetrators of the Sept. 11 attacks. Avon Twitty, for example, was serving a 27-year sentence for killing a man during an argument before being transferred to a CMU for the final years of his sentence, but he was also a convert to Islam.

According to a lawsuit filed by the Center for Constitutional Rights on behalf of a number of prisoners, the CMUs are analogous to solitary confinement — an “experiment in social isolation” that allows corrections officials to retaliate against what they view as bad behavior, even if it is protected by the First Amendment. By classifying the CMUs as simply a way to monitor inmates, rather than as a punishment, the Bureau of Prisons has sidestepped the knotty issue of due process rights.

In a bit of what McGowan’s lawyer at the Center for Constitutional Rights, Rachel Meeropol, calls “beautiful doublespeak,” the BOP refers to the CMUs as “self-contained general population units.” The inmates may be quarantined in the CMUs, the BOP asserts, but the units are still “general population” and thus don’t require additional administrative procedures to determine which prisoners will be placed there.

“My suspicion from the get-go was, I’m unrepentant in terms of my political identity,” McGowan says of his placement in the CMU. “I think what they’re trying to do is say, ‘OK, you want to be a little political prisoner type, you want to write and be all active and say stuff, and get a ton of mail and everyone thinks you’re peachy keen? You’re gonna get crushed.'”

The Bureau of Prisons has strenuously denied that it places inmates in CMUs because they are Muslim or because they have exercised other First Amendment rights. “Inmates are designated to the unit for management of their communications based on the potential security threat they present,” Chris Burke, a BOP spokesman, wrote in a statement to The Huffington Post. At least some inmates, he added, may be placed in the units for other communications threats, like trying to harass victims or witnesses of their crimes.

McGowan, at first blush, does not fit the image of a terrorist. Born the son of a police officer in New York’s working-class Rockaway neighborhood, he attended the State University of New York in Buffalo and then drifted into the world of environmental activism. In the hothouse atmosphere of Eugene, Ore., in the late 1990s, he became more and more radicalized — an evolution detailed in the Oscar-nominated documentary “If a Tree Falls” — and eventually joined a small cell of the Earth Liberation Front.

McGowan and his group conducted a campaign of vandalism and arson across the Pacific Northwest for several years. No one was killed or injured. Eventually, McGowan says, while his hands were still covered in gasoline during one of their actions, he decided to split from the group. In 2002, the year in which he turned 28, he moved back home to New York and took a job at a Brooklyn nonprofit for victims of domestic violence.

McGowan met Synan at his sister’s birthday party just before he moved back, and he was instantly taken with her. They began dating. She was sitting at work at an arts organization in December 2005 when she received a call from one of McGowan’s office mates that he had just been taken away by FBI agents. “And that was the first that I knew” that McGowan might have been under investigation, she says.

McGowan’s autonomous cell within the decentralized Earth Liberation Front was known as “The Family.” Its members had promised never to turn on each other if the feds came calling. But one of them did, leading to indictments for McGowan and six of his companions.

After bail, house arrest and legal proceedings — protracted because he refused to testify against his fellow defendants — McGowan eventually agreed to enter a non-cooperation plea. He would admit to taking part in arsons at a lumber company and a tree farm, but he would not be forced to testify against his fellow defendants.

“I hope that you will see that my actions were not those of [a] terrorist but of a concerned young person,” McGowan said in his plea statement in November 2006. “After taking part in these two actions, I realized that burning things down did not fit with my visions or belief about how to create a better world. So I stopped committing these crimes.”

McGowan did not see himself as a terrorist, but the federal government did. In the midst of a nationwide panic over environmentalist-linked crimes that critics call “the green scare,” prosecutors obtained a terrorism enhancement for McGowan’s crimes. The designation did not result in a longer prison term, but McGowan’s supporters warned that it could lead to his placement in one of the CMUs, which were just being set up at the time.

Civil liberties groups like the National Lawyers Guild and criminal defense attorneys were infuriated by the “terrorist” label, which McGowan rejects to this day. Although they may not have approved of his criminal tactics, they argued that labeling him a terrorist was an absurd overreaction to crimes that resulted in nothing more than property damage.

“Is this what a terrorist is?” Heidi Boghosian, executive director of the National Lawyers Guild, asked at the time. “Americans know the difference between Daniel McGowan and Osama bin Laden, and this effort to subvert the fairness of the judicial system is an affront to the values they hold dear.”

Still, as McGowan was serving his sentence at Sandstone, Leslie Smith, the chief of the prison system’s Counter-Terrorism Unit, made the case to have him transferred to a more restrictive facility and to have his communications cut off. In a memo dated March 27, 2008, Smith argued that McGowan was an “organizer.”

“While incarcerated and through social correspondence and articles written for radical publications, inmate McGowan has attempted to unite the radical environmental and animal liberation movements,” Smith wrote. McGowan, according to Smith, had spoken bitterly of the government’s cooperating witnesses as “snitches” for their “betrayal.”

“We need to have serious conversations about whether militancy is truly effective in all situations,” McGowan told the Earth First! Journal. “Certainly, direct action is a wonderful tool, but from my experience, it may not be the most effective one at all times or in all situations.”

“Direct action” is a deliberately vague term that covers a wide range of protest tactics, from non-violent sit-ins to sabotage and property destruction. But for those versed in the movement’s lingo, it was clear what McGowan was saying: Think twice before you try actions as aggressive as mine.

Nevertheless, to Smith, those articles and interviews about “direct action” were proof positive that McGowan was trying to act as a “spokesman” for the radical environmental movement.

According to Burke, the BOP spokesman, inmates can be placed in CMUs when they “have been convicted of, or associated with, international or domestic terrorism,” when they “attempt to coordinate illegal activities via approved communication methods while incarcerated,” or when they “have extensive disciplinary histories for the continued misuse/abuse of approved communication methods.”

In his memo, Smith noted McGowan’s sterling disciplinary history but emphasized his speech since entering prison. Two months later, he was on the bus out of Sandstone.

In McGowan’s words, he “got snatched.”

* * * * *At Marion, McGowan says, he found a totally different world from the one he had known at Sandstone. With severely limited contact with the outside, and little access to the classes and activities available at regular prisons, inmates would stare at the TV all day or wander the halls aimlessly, like zombies.

When his wife visited him, they could no longer kiss and hug and play board games. Instead, they would walk down a hallway together, with two sets of bars between them, unable to touch. In a small room, they would sit across from each other, separated by glass, and speak through phones, so that agents in the BOP’s Counter-Terrorism Unit could listen in.

“The worst part would be in the hallway together, and it’d be like two sets of bars, and she’d be coming in and I’d be going in the same room, and I’d see her in the flesh and I’d go I can’t even believe how insane this is,” McGowan remembers thinking. “Because then we go into our little box, and there’s two cameras, and you’re on a crappy little phone.”

“And then you go there and you’re behind glass,” Synan says. “You can’t touch the other person, feel their hands, touch their skin. But also you’re sitting there in a very tiny booth, holding a phone, knowing that there’s somebody recording the call.”

Other families broke apart under the strain, McGowan says. His relationship with Synan, whom he married shortly before his prison term began, was tested.

At the time, only 15 minutes were allotted for phone time each week, making conversations frustrating. “Say you’re just bickering about something, but after 15 minutes that phone hangs up, but you get nothing for the next week,” Synan says. “You have to just sit there and, say somehow, we’re in the middle of this argument, but you can’t do anything about it.”

Most difficult for McGowan, Synan says, was when his mother died in 2009. On their one phone call a week, she told him that his mother was in the hospital. “Your mom’s very sick,” she said. “It’s just a matter of time.”

But McGowan needed to have the hospital’s phone number approved before he could call it — a process that couldn’t be completed late on a Friday. All through the weekend, he lived in a suspended state, waiting for Monday to find out whether his mother was dead.

“It’s horrible. This is life and death, and they had to approve a hospital room phone number, which is ridiculous,” Synan says.

McGowan’s mother made it through the weekend — a small solace. He called the hospital room, and with his sisters holding up the phone on the other end to his barely speaking mother, he talked to her. “He’s got 15 minutes and that’s it,” Synan recalls. “And so the phone hangs up and he’s talked to his mom, and he won’t know anything for a while.”

“That was the only way to do it,” Synan says. McGowan had made her promise she would let him know as soon as possible.

With a few interruptions, McGowan was held in the CMU at Marion for two years. In October 2010, he was released into the prison’s general population.

But McGowan’s time in Little Guantanamo was far from over. After several months in general population, in February 2011 he was sent off to the other CMU, housed on the old death row at the Federal Correctional Complex in Terre Haute. McGowan says that move also smacked of retaliation and further highlighted the absurdity of treating prisoners like dangerous terrorists one day and common criminals the next.

The reason for his second transfer seems Kafkaesque. In January 2011, the leaks website Public Intelligence released two BOP Counter-Terrorism intelligence reports, which included details on letters to many of the inmates held at the CMUs. The documents provided a rare look into just what sort of communications monitoring the BOP was conducting on its “terrorist” inmates, including McGowan.

In one week, the report detailed, McGowan received two items of interest to the BOP: a series of postcards from a woman at a G-8 summit in Italy, describing the demonstrations there as “boring and depressing” because of their “total lack of antagonism,” and a letter from a lawyer describing an animal rights conference at which the “green scare” and McGowan’s incarceration were discussed.

Another report said that McGowan had been mailed a copy of a radical environmentalist magazine, which prison officials rejected, and an email from a member of a social justice public relations collective. “Much respect to you for hanging in there and staying strong,” Ryan Fletcher wrote to McGowan on Aug. 7, 2009. “One day all of this will come out and expose this thing for what it is.”

The BOP delivered some of these messages to McGowan and rejected others as too inflammatory for prison. But with the reports about his communications now live on the Internet for anyone to see, McGowan asked his wife to have his lawyer mail him copies.

To the BOP, that was “circumventing monitoring through the use of legal mail.” McGowan was sent to the Terre Haute CMU, where he spent the next 22 months.

* * * * *In December 2012, in the final months of his seven-year sentence, McGowan was released to a halfway house in Brooklyn and obtained a job manning the front desk of a law firm.

But even then, he and his lawyers say, he was not free from the prison system’s efforts to retaliate against him.

On April 1, 2013, McGowan wrote a blog post for The Huffington Post about his incarceration in the CMUs. Three days later, U.S. marshals showed up at his halfway house. He was taken to the Metropolitan Detention Center in Brooklyn and placed in solitary confinement.

For McGowan, his wife and his lawyers, what followed were 20 hours of terror. They had no idea whether he was about to be shipped back to one of the CMUs. They had no idea, other than perhaps the blog post, why the BOP was so upset with him.

McGowan’s jailing provoked protests from his lawyers and was reported across the Internet, including HuffPost and Politico. Three different BOP officials gave HuffPost three different explanations as to what was happening and why. Barely a day later, perhaps realizing the public relations mess it was causing, the Bureau of Prisons released McGowan back to his halfway house. Federal officials later admitted that McGowan’s re-entry manager had jailed him on the basis of a regulation barring prisoners from speaking to the media — a regulation that had been ruled unconstitutional in 2007.

To McGowan, the episode was a reminder of just how arbitrary and over-the-top the BOP’s reaction to political speech can be.

“The irony is just so thick,” McGowan says. “You’re writing an article about retaliation for freedom of speech and writing, and they retaliate by throwing you in prison.”

If the prison system was hoping to break McGowan’s will to express himself by sending him to the CMUs, or by jailing him for his blog posts, it failed. McGowan vows that his experience will only make him fight harder for the environment. It has also given him a new cause to fight for: prison reform.

In July, a federal judge ruled that McGowan could no longer participate in the Center for Constitutional Rights’ lawsuit against the federal prison system, in large part because he is no longer a prisoner. But he is not the only one to have faced retaliation, the suit alleges.

Kifah Jayyousi is a Detroit native and Navy veteran who became a supporter of the Blind Sheik. Convicted in 2007 of conspiracy to murder, kidnap and maim in a foreign country and to provide material support to al-Qaeda, he was sentenced to 12 years in prison.

Jayyousi has never been accused of trying to communicate with al-Qaeda or any other terrorist group while in prison. But in June 2008, Smith had him transferred from a Florida prison to the Terre Haute CMU based on his conviction for a terrorism-related crime.

Inside the unit, Jayyousi became a leader among his fellow Muslims. Two months after his arrival, in the middle of the heated presidential election, Jayyousi delivered a sermon to the other prisoners.

“You were brought here because you are Muslim and … our response to that has to be to stand firm, stand strong, to stand steadfast,” Jayyousi said, according to the BOP’s transcript of his monitored speech. “John McCain is a presidential candidate, and in two months he could be our president. Where was he 20 years ago? He was being tortured in a Vietnamese prison for many years with no hope. … He stood fast, he stayed firm, he came through.”

“You are going to return to your Lord to meet him with your hard work and the hardships that you have faced and done in this life; this is why we martyr,” Jayyousi said.

In October 2010, when one of his original co-defendants was sent to Terre Haute, Jayyousi was shipped off to Marion. The CMU unit manager there recommended him for release into the general population in February 2011, citing “clear conduct and a good rapport with staff and other inmates” and “no continuation of actions which precipitated his placement in the CMU.” But Smith again interceded.

“Jayyousi made statements which were aimed at inciting and radicalizing the Muslim inmate population in [the] CMU,” Smith wrote. In Smith’s characterization, Jayyousi’s long statement about prison conditions — which cited McCain; the late Vice Adm. James Stockdale, another Vietnam POW; and Nelson Mandela — was transformed into a call for inmates to “martyr themselves to serve Allah.”

Jayyousi claims, according to the Center for Constitutional Rights lawsuit, that he was simply standing up for himself and other Muslim inmates who had been put in prison and the CMU because of “fabricated” terrorism convictions. But Smith said the speech was a “highly inflammatory” action from a “charismatic leader” that “encouraged activities which would lead to a group demonstration.”

The debate is important, because courts have long held that prison officials may take actions limiting the free speech of inmates if those actions also advance “legitimate penological objectives,” such as disrupting potential prison riots.

“The Constitution applies to prisoners too,” says Meeropol of the Center for Constitutional Rights. “When you’re put in prison, there are a lot of limits on your rights … but there are limits on what can be done to them.”

In July, a federal judge found that Jayyousi had a “plausible claim” that he had suffered retaliation because of his speech. “There is arguably a disparity between the actual content of the sermon and Smith’s description of it,” the judge wrote.

Jayyousi remained in the Marion CMU until May 2013, when he was released into the general population at Marion. He “was not provided with any explanation,” Meeropol says.

Although Meeropol is glad that the BOP has instituted procedures for moving inmates out of the CMUs — in fact, the first time a prisoner was released from a CMU was when the BOP let one of her group’s named plaintiffs out a week before the group launched its lawsuit — she still calls the situation of alleged hardened terrorists being moved in and out of the general population “ridiculous.”

“There’s no clear criteria for how a prisoner can earn their way out of the CMU,” Meeropol says.

“When you don’t have procedural protections in place, it’s not surprising that abuse would result,” she adds. “The retaliation comes in with a case like Daniel.”

On June 6, McGowan was released from the halfway house after seven years in the Bureau of Prisons’ custody. At 6:01 a.m., he left the house. He got on the subway and finally headed home to crawl into bed with his wife. That weekend they stayed in at a fancy hotel. Since then, he says, he’s enjoyed simple pleasures like rock concerts — the Postal Service and Black Flag, two bands that have been re-formed since he was incarcerated — and his niece’s birthday party on Long Island.

Other than that, McGowan says, “it’s very early, and I’m trying to get my head straight about just being out and living my life. Trying to get through each day.”